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Abstract CRISPR-based genome editing of pseudogene-associated disorders, such as p47 phox -deficient chronic granulomatous disease (p47 CGD), is challenged by chromosomal rearrangements due to presence of multiple targets. We report that interactions between highly homologous sequences that are localized on the same chromosome contribute substantially to post-editing chromosomal rearrangements. We successfully employed editing approaches at the NCF1 gene and its pseudogenes, NCF1B and NCF1C, in a human cell line model of p47 CGD and in patient-derived human hematopoietic stem and progenitor cells. Upon genetic engineering, a droplet digital PCR-based method identified cells with altered copy numbers, spanning megabases from the edited loci. We attributed the high aberration frequency to the interaction between repetitive sequences and their predisposition to recombination events. Our findings emphasize the need for careful evaluation of the target-specific genomic context, such as the presence of homologous regions, whose instability can constitute a risk factor for chromosomal rearrangements upon genome editing.

Abstract The outcome of CRISPR-Cas-mediated genome modifications is dependent on DNA double-strand break (DSB) processing and repair pathway choice. Homology-directed repair (HDR) of protein-blocked DSBs requires DNA end resection that is initiated by the endonuclease activity of the MRE11 complex. Using reconstituted reactions, we show that Cas9 breaks are unexpectedly not directly resectable by the MRE11 complex. In contrast, breaks catalyzed by Cas12a are readily processed. Cas9, unlike Cas12a, bridges the broken ends, preventing DSB detection and processing by MRE11. We demonstrate that Cas9 must be dislocated after DNA cleavage to allow DNA end resection and repair. Using single molecule and bulk biochemical assays, we next find that the HLTF translocase directly removes Cas9 from broken ends, which allows DSB processing by DNA end resection or non-homologous end-joining machineries. Mechanistically, the activity of HLTF requires its HIRAN domain and the release of the 3′-end generated by the cleavage of the non-target DNA strand by the Cas9 RuvC domain. Consequently, HLTF removes the H840A but not the D10A Cas9 nickase. The removal of Cas9 H840A by HLTF explains the different cellular impact of the two Cas9 nickase variants in human cells, with potential implications for gene editing.

Abstract Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon ‘Candidatus Harpocratesius repetitus’ shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.

Summary: Myasthenia gravis (MG) is etiologically associated with thymus abnormalities, but its pathology in the thymus remains unclear. In this study, we attempt to narrow down the features associated with MG using spatial transcriptome analysis of thymoma and thymic hyperplasia samples. We find that the majority of thymomas are constituted by the cortical region. However, the small medullary region is enlarged in seropositive thymomas and contains polygenic enrichment and MG-specific germinal center structures. Neuromuscular medullary thymic epithelial cells, previously identified as MG-specific autoantigen-producing cells, are enriched in the cortico-medullary junction. The medulla is characterized by a specific chemokine pattern and immune cell composition, including migratory dendritic cells and effector regulatory T cells. Similar germinal center structures and immune microenvironments are also observed in the thymic hyperplasia medulla. This study shows that the medulla and junction areas are linked to MG pathology and provides insights into future MG research.

Abstract Prime editing is a highly versatile genome editing technology that enables the introduction of base substitutions, insertions, and deletions. However, compared to traditional Cas9 nucleases prime editors (PEs) are less active. In this study we use OrthoRep, a yeast-based platform for directed protein evolution, to enhance the editing efficiency of PEs. After several rounds of evolution with increased selection pressure, we identify multiple mutations that have a positive effect on PE activity in yeast cells and in biochemical assays. Combining the two most effective mutations – the A259D amino acid substitution in nCas9 and the K445T substitution in M-MLV RT – results in the variant PE_Y18. Delivery of PE_Y18, encoded on DNA, mRNA or as a ribonucleoprotein complex into mammalian cell lines increases editing rates up to 3.5-fold compared to PEmax. In addition, PE_Y18 supports higher prime editing rates when delivered in vivo into the liver or brain. Our study demonstrates proof-of-concept for the application of OrthoRep to optimize genome editing tools in eukaryotic cells.

Abstract CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential mechanism in which initial cleavage of the non-target strand is followed by target strand cleavage. How the spatially distant DNA target strand traverses toward the RuvC catalytic core is presently not understood. Here, continuous tens of microsecond-long molecular dynamics and free-energy simulations reveal that an α-helical lid, located within the RuvC domain, plays a pivotal role in the traversal of the DNA target strand by anchoring the crRNA:target strand duplex and guiding the target strand toward the RuvC core, as also corroborated by DNA cleavage experiments. In this mechanism, the REC2 domain pushes the crRNA:target strand duplex toward the core of the enzyme, while the Nuc domain aids the bending and accommodation of the target strand within the RuvC core by bending inward. Understanding of this critical process underlying Cas12a activity will enrich fundamental knowledge and facilitate further engineering strategies for genome editing.

Abstract Peatland vegetation takes up mercury (Hg) from the atmosphere, typically contributing to net production and export of neurotoxic methyl-Hg to downstream ecosystems. Chemical reduction processes can slow down methyl-Hg production by releasing Hg from peat back to the atmosphere. The extent of these processes remains, however, unclear. Here we present results from a comprehensive study covering concentrations and isotopic signatures of Hg in an open boreal peatland system to identify post-depositional Hg redox transformation processes. Isotope mass balances suggest photoreduction of HgII is the predominant process by which 30% of annually deposited Hg is emitted back to the atmosphere. Isotopic analyses indicate that above the water table, dark abiotic oxidation decreases peat soil gaseous Hg0 concentrations. Below the water table, supersaturation of gaseous Hg is likely created more by direct photoreduction of rainfall rather than by reduction and release of Hg from the peat soil. Identification and quantification of these light-driven and dark redox processes advance our understanding of the fate of Hg in peatlands, including the potential for mobilization and methylation of HgII.

Abstract Background As in most solid cancers, the emergence of cells with oncogenic mutations in the mammary epithelium alters the tissue homeostasis. Some soluble factors, such as TGFβ, potently modify the behavior of healthy stromal cells. A subpopulation of cancer-associated fibroblasts expressing a TGFβ target, the SNAIL1 transcription factor, display myofibroblastic abilities that rearrange the stromal architecture. Breast tumors with the presence of SNAIL1 in the stromal compartment, and with aligned extracellular fiber, are associated with poor survival prognoses. Methods We used deep RNA sequencing and biochemical techniques to study alternative splicing and human tumor databases to test for associations (correlation t-test) between SNAIL1 and fibronectin isoforms. Three-dimensional extracellular matrices generated from fibroblasts were used to study the mechanical properties and actions of the extracellular matrices on tumor cell and fibroblast behaviors. A metastatic mouse model of breast cancer was used to test the action of fibronectin isoforms on lung metastasis. Results In silico studies showed that SNAIL1 correlates with the expression of the extra domain A (EDA)-containing (EDA+) fibronectin in advanced human breast cancer and other types of epithelial cancers. In TGFβ-activated fibroblasts, alternative splicing of fibronectin as well as of 500 other genes was modified by eliminating SNAIL1. Biochemical analyses demonstrated that SNAIL1 favors the inclusion of the EDA exon by modulating the activity of the SRSF1 splicing factor. Similar to Snai1 knockout fibroblasts, EDA- fibronectin fibroblasts produce an extracellular matrix that does not sustain TGFβ-induced fiber organization, rigidity, fibroblast activation, or tumor cell invasion. The presence of EDA+ fibronectin changes the action of metalloproteinases on fibronectin fibers. Critically, in an mouse orthotopic breast cancer model, the absence of the fibronectin EDA domain completely prevents lung metastasis. Conclusions Our results support the requirement of EDA+ fibronectin in the generation of a metastasis permissive stromal architecture in breast cancers and its molecular control by SNAIL1. From a pharmacological point of view, specifically blocking EDA+ fibronectin deposition could be included in studies to reduce the formation of a pro-metastatic environment.

Abstract CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.

Maintaining biodiversity in agricultural landscapes is a major challenge for environmental protection in Europe. Vineyards rely heavily on agrotechnical interventions such as herbicide use and tillage for weed control, which affect biodiversity and can lead to soil erosion and resistant weed populations. The fragmentation of agricultural landscapes affects biodiversity by altering community composition and often reducing plant population sizes and genetic diversity. However, it can also increase the abundance of certain species and enhance population resilience to environmental change. Vineyards can support high levels of biodiversity and provide ecosystem services due to their semi-natural habitat structure. This research evaluates vegetation biodiversity using phytosociological relevés in different vineyards. Our results show that species richness and biodiversity are significantly influenced by vineyard age and management type. This study highlights differences in the representation of plant functional groups, with perennial taxa in grassy inter-row contributing to anti-erosion functions and serving as food sources for pollinators. The root zone around vine trunks shows an increase in invasive species with vineyard age, posing a risk to the agroecosystem. Vineyards predominantly follow a ruderal ecological strategy, using nutrients and light efficiently, while tolerating management disturbances. Understanding these dynamics is critical for developing sustainable vineyard management practices that support biodiversity and ecological resilience, counteract the homogenization of agricultural landscapes, and promote the coexistence of viticulture and species-rich ecosystems.

Abstract Fabrication of highly aligned fibers by far-field electrospinning is a challenging task to accomplish. Multiple studies present advances in the alignment of electrospun fibers which involve modification of the conventional electrospinning setup with complex additions, multi-phased fabrication, and expensive components. This study presents a new collector design with an origami structure to produce highly-aligned far-field electrospun fibers. The origami collector mounts on the rotating drum and can be easily attached and removed for each round of fiber fabrication. This simple, effective, and inexpensive technique yields high-quality ultra-aligned fibers while the setup remains intact for other fabrication types. The electrospun poly(ɛ-caprolactone) (PCL) fibers were assessed by scanning electron microscope (SEM), fiber diameter distribution, water contact angle (WCA), Fast Fourier Transform analysis (FFT), surface plot profile, and pixel intensity plots. We thoroughly explored the impact of influential parameters, including polymer concentration, injection rate, collector rotation speed, distance from the collector to the tip, and needle gauge number on fibers’ quality and alignment. Moreover, we employed machine learning algorithms to predict the outcomes and classify the high-quality fibers instead of low-quality productions.

We investigated Hg accumulation in maize (Zea mays) plants grown in non-contaminated conditions on a farm in Switzerland throughout a growing season. Concentrations of Hg in leaves and husk followed the same temporal pattern as the mass growth of these parts. In contrast, silk and tassel accumulated Hg almost linearly over time until harvest. At the end of the growing season Hg concentration was highest in tassel (10.4 ng g−1), followed by leaves (7.3 ng g−1) and silk (5.7 ng g−1). Silk and tassel had accumulated 5–10 times more Hg per unit dry mass than all aboveground parts of the plant on average. Cob and kernels contained only very small amounts of Hg. Greater exposure of a plant part to the atmosphere was clearly associated with higher rates of Hg accumulation.

Sugar beet production is highly affected by weeds. The structure of crop rotation, the use of intercrops and different tillage techniques bring several benefits to sugar beet cultivation and create different living conditions for weeds. The response of weed communities in sugar beet stands has not been studied. The experimental plot is in the cadastral area of Ivanovice na Hané (Czech Republic). During an eight-year monitoring period (2013–2020), 46 weed species were identified. The dominant species was Chenopodium album. There were also summer and winter weeds. A more varied crop rotation increased the intensity of weed infestation, with winter weeds being the most common. On the contrary, a higher proportion of cereals in the crop structure favors the presence of summer weeds. The tillage technology and the inclusion of catch crops did not significantly affect the intensity of weed infestation in sugar beet stands or the spectrum of weed species. Current cropping technologies have driven the evolution of weeds. Due to their short life cycles and relatively simple genomes, weeds can respond very quickly to technological measures and, thus, change their harmfulness.

En este artículo se presenta un modelo para simular y predecir la máxima demanda semanal de un sector de la red de distribución de agua de la ciudad de Guanajuato. El modelo está compuesto de dos submodelos, uno determinístico y uno estocástico, los cuales se calibran con datos históricos de la demanda. El submodelo determinístico está descrito por la serie de Fourier, mientras que el submodelo estocástico involucra la función cuantil de la distribución log-logística. Con el fin de probar la capacidad del modelo para describir el comportamiento de la demanda, se utilizaron datos para calibrar y validar el modelo, los cuales fueron proporcionados por un sistema holístico de telemetría. Dicho sistema consta de una red de estaciones para la medición y registro de datos, así como de un sistema de almacenamiento y procesamiento de la información.

Abstract Dysbiosis of the oral microbiome mediates chronic periodontal disease. Realignment of microbial dysbiosis towards health may prevent disease. Treatment with antibiotics and probiotics can modulate the microbial, immunological, and clinical landscape of periodontal disease with some success. Antibacterial peptides or bacteriocins, such as nisin, and a nisin-producing probiotic, Lactococcus lactis, have not been examined in this context, yet warrant examination because of their biomedical benefits in eradicating biofilms and pathogenic bacteria, modulating immune mechanisms, and their safety profile in humans. This study’s goal was to examine the potential for nisin and a nisin-producing probiotic to abrogate periodontal bone loss, the host inflammatory response, and changes in oral microbiome composition in a polymicrobial mouse model of periodontal disease. Nisin and a nisin-producing Lactococcus lactis probiotic significantly decreased the levels of several periodontal pathogens, alveolar bone loss, and the oral and systemic inflammatory host response. Surprisingly, nisin and/or the nisin-producing L. lactis probiotic enhanced the population of fibroblasts and osteoblasts despite the polymicrobial infection. Nisin mediated human periodontal ligament cell proliferation dose-dependently by increasing the proliferation marker, Ki-67. Nisin and probiotic treatment significantly shifted the oral microbiome towards the healthy control state; health was associated with Proteobacteria, whereas 3 retroviruses were associated with disease. Disease-associated microbial species were correlated with IL-6 levels. Nisin or nisin-producing probiotic’s ability to shift the oral microbiome towards health, mitigate periodontal destruction and the host immune response, and promote a novel proliferative phenotype in reparative connective tissue cells, addresses key aspects of the pathogenesis of periodontal disease and reveals a new biomedical application for nisin in treatment of periodontitis and reparative medicine.

The Czech Republic took over the presidency of the European Union Council from France during a deep crisis ignited by the aggressive Russian invasion of Ukraine. In fact, as a result of the invasion, the Czech presidency had to deal with a multitude of crises: not only the actual security crisis, that is, Russian forces attacking a country at the EUʼs border, but also an energy crisis manifested by price hikes and supply insufficiency, and an economic crisis caused by both of the above. As energy was among the priorities of the presidency, the article focuses on this area, assessing the presidencyʼs performance in strengthening the blocʼs energy security. The text focuses on electricity and natural gas markets, given the impact of the crisis on these areas and the fact that their functioning is communitarized. Retrospectively, it also takes on the topic of what the presidencyʼs main message and legacy were when it passed the proverbial baton to Sweden at the end of 2022. The research found that the agreements reached under the Czech presidency can increase the Unionʼs energy security, namely the availability and affordability of energy supplies. The presidency also showcased the Czech Republic’s ability to achieve broad agreement even on controversial points.

The primary measures against radon in buildings are a tight contact structure or venting the subsoil beneath the building. In many cases, ventilation systems used in buildings to ensure good indoor air quality can also be used to reduce the radon concentration. This study aims to evaluate the environmental impacts of residential ventilation systems for their ability to lower the concentration of this gas. The life cycle assessment methodology was used to assess two kinds of ventilation systems. The results indicate that 95% of environmental impacts are associated with operational emissions, while 5% are associated with embodied ones. Moreover, an increase in radon supply rates resulted in an increase in energy consumption and related emissions, for example, the operational energy of an exhaust ventilation system aimed for a reduction to 200 Bq/m3 in a 9/15 cyclic mode range from 9.69 for a radon supply rate of 50 Bq/m3h to 32.27 for 200 Bq/m3h. These simulations show that ventilation systems cannot be considered universally suitable measures to reduce the radon concentration because they may become very energy demanding, and their environmental impact may be significant even considering the type of energy source. Based on this study, we can determine whether it makes sense for a given radon supply rate and energy source to use a ventilation system to reduce the radon concentration in residential buildings.

3′ end formation of most eukaryotic mRNAs is dependent on the assembly of a ~1.5 MDa multiprotein complex, that catalyzes the coupled reaction of pre-mRNA cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) constitutes the core of the 3′ end processing machinery onto which the remaining factors, including cleavage stimulation factor (CstF) and poly(A) polymerase (PAP), assemble. These interactions are mediated by Fip1, a CPSF subunit characterized by high degree of intrinsic disorder. Here, we report two crystal structures revealing the interactions of human Fip1 (hFip1) with CPSF30 and CstF77. We demonstrate that CPSF contains two copies of hFip1, each binding to the zinc finger (ZF) domains 4 and 5 of CPSF30. Using polyadenylation assays we show that the two hFip1 copies are functionally redundant in recruiting one copy of PAP, thereby increasing the processivity of RNA polyadenylation. We further show that the interaction between hFip1 and CstF77 is mediated via a short motif in the N-terminal ‘acidic’ region of hFip1. In turn, CstF77 competitively inhibits CPSF-dependent PAP recruitment and 3′ polyadenylation. Taken together, these results provide a structural basis for the multivalent scaffolding and regulatory functions of hFip1 in 3′ end processing.

The E3 ligase Hakai can interact with the m6A methylation machinery but its function is still unclear. Here, the authors show that Hakai is a conserved component of the m6A methyltransferase complex and provide functional and molecular insights into its role in regulating m6A levels in Drosophila.

For the past decades, broad questions as to “what is Islam” and “what does it mean to be Islamic” have haunted much of the fields of sociology and anthropology of Islam, arousing vigorous conceptual and methodological dialectics in scholarship. Without centralizing the conceptual problematic in the first place, and without being confined to the preceding theoretical struggles, Kamaludeen Mohamed Nasir’s Representing Islam: Hip-Hop of the September 11 Generation, a cultural and social hermeneutic of the synthesis between Islamic religiosity and hip-hop culture as practiced and perceived by Muslim youth around the world, nevertheless provides interesting answers, in both conceptual and empirical forms, to these primordial questions. It sheds new light on understanding and interpreting the articulation, manifestations, and implications of and about Islam in this globalized and digitalized age.

Book review: Jan Černý, Jevení a spása, Subjektivita v materiální fenomenologii Michela Henryho, Praha (Filosofia) 2019, 255 str.

Annual ryegrass (Lolium multiflorum var. westerwoldicum) is cultivated in various areas of the world as a feed for live stock. Efforts to improve the production of high-quality feed in the face of deepening climate change have increased the demand for growing non-traditional types of crops, including ryegrass. The aims of the research were to determine the spectrum of weed and fungal pathogen species and to assess dangerous species of weeds and pathogens which negatively affect forage crops of annual ryegrass grown in dry conditions. In 2018-2019 the occurrence of weeds and fungal pathogens of ryegrass was evaluated in field conditions. The assessed lands were located in dry climatic conditions of South Moravia (Czech Republic). The vegetation recording was done on phytosociological plots of 12 m2. A total of 57 weed species were identified in the plots, where 12 species were toxic and 16 species were undesirable. The most problematic weeds and poisonous species were: Aethusa cynapium, Datura stramonium, Equisetum palustre, Euphorbia helioscopia, Fumaria officinalis and Solanum nigrum, which can cause health problems if present in cattle feed. A pathogenic infection caused by Blumeria graminis, Puccinia graminis var. graminicola and P. coronata var. coronata, Gaeumannomyces graminis and Drechslera sp. was identified on the ryegrass plants in the experimental plots during the vegetation. Blumeria graminis was the most abundant, but it did not endanger the final feed. The data was processed by CCA analysis.

Colloidal matrices of native and oxidized pectin were developed to improve iron bioavailability through the digestive tract. Ferrous bisglycinate (Gly-Fe), obtained by precipitation of glycine chelation to Fe2+, was mixed with native and peroxide-oxidized citrus pectin, and subsequently lyophilized. Controls included matrices with iron and glycine without chelation. The resulting samples were characterized through FTIR, SEM, and TGA/DSC before and after in vitro digestion, which was performed in simulated salivary, gastric, and intestinal fluids. During these digestions, swelling capacity and iron release were assessed. All matrix formulations were porous, and while pectin oxidation did not alter architecture, it changed their properties, increasing thermal stability, likely due to greater number of interaction possibilities through carbonyl groups generated during oxidation. This also resulted in lower swelling capacity, with greater stability observed when using the chelated complex. Higher swelling was found in gastric and intestinal fluids. Pectin oxidation also increased retention of the chelated form, contrary to what was observed with unchelated iron. Thus, there is an important effect of pectin oxidation combined with iron in the form of ferrous biglyscinate on matrix stability and iron release through the digestive tract. These matrices could potentially improve iron bioavailability, diminishing organoleptic changes in fortified iron foods.

Seasonal patterns of molecular markers in humans have not been extensively studied. Here, the authors combine host components (transcriptome, metabolome, proteome, immunome, clinical lab tests) and microbiome to profile 105 individuals, identifying over 1000 markers in two major seasonal patterns.

Resurrection of non-processed pseudogenes may increase the efficacy of therapeutic gene editing, upon simultaneous targeting of a mutated gene and its highly homologous pseudogenes. To investigate the potency of this approach for clinical gene therapy of human diseases, we corrected a pseudogene-associated disorder, the immunodeficiency p47phox-deficient chronic granulomatous disease (p47phox CGD), using clustered regularly interspaced short palindromic repeats-associated nuclease Cas9 (CRISPR-Cas9) to target mutated neutrophil cytosolic factor 1 (NCF1). Being separated by less than two million base pairs, NCF1 and two pseudogenes are closely co-localized on chromosome 7. In healthy people, a two-nucleotide GT deletion (ΔGT) is present in the NCF1B and NCF1C pseudogenes only. In the majority of patients with p47phox CGD, the NCF1 gene is inactivated due to a ΔGT transfer from one of the two non-processed pseudogenes. Here we demonstrate that concurrent targeting and correction of mutated NCF1 and its pseudogenes results in therapeutic CGD phenotype correction, but also causes potentially harmful chromosomal deletions between the targeted loci in a p47phox-deficient CGD cell line model. Therefore, development of genome-editing-based treatment of pseudogene-related disorders mandates thorough safety examination, as well as technological advances, limiting concurrent induction of multiple double-strand breaks on a single chromosome.

Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic oligoadenylates that activate effectors such as Csm6 ribonucleases. Here, Garcia-Doval et al. show that Enteroccocus italicus Csm6 degrades its cyclic hexa-AMP activator, and report the crystal structure of the protein bound to an activator mimic.

For single-cell RNA-seq experiments the sequencing budget is limited, and how it should be optimally allocated to maximize information is not clear. Here the authors develop a mathematical framework to show that, for estimating many gene properties, the optimal allocation is to sequence at the depth of one read per cell per gene.

In this work, we reviewed our results on the prospect of increasing the quality of ion acceleration driven by high-intensity laser pulses using low-Z structured targets. It is shown that the radiation pressure acceleration mechanism dominates over target normal sheath acceleration for assumed laser target parameters when the laser intensity is high enough. The target thickness is optimized for this regime and double-layer structure is investigated. When a corrugation is fabricated on the interface of such a target, a relativistic instability with Rayleigh–Taylor and Richtmyer–Meshkov like features can be driven by the target interaction with a high intensity laser pulse. The proper development of this instability leads to the generation of a collimated quasi-monoenergetic ion beam with lower emittance, divergence, and energy spread compared to a single and double-layer target with planar interface. A steep-front laser pulse is used in our simulations to mitigate other type of instabilities arising at the target surface from the laser–target interaction. We discuss the use of a plasma shutter to generate the required pulse profile, which also locally increases intensity. The obtained shape improves the ion acceleration, including higher maximal energy and lower beam divergence, in our simulation of a high-Z target.

RtcB enzymes are RNA ligases that play essential roles in tRNA splicing, unfolded protein response, and RNA repair. In metazoa, RtcB functions as part of a five-subunit tRNA ligase complex (tRNA-LC) along with Ddx1, Cgi-99, Fam98B, and Ashwin. The human tRNA-LC or its individual subunits have been implicated in additional cellular processes including microRNA maturation, viral replication, DNA double-strand break repair, and mRNA transport. Here, we present a biochemical analysis of the inter-subunit interactions within the human tRNA-LC along with crystal structures of the catalytic subunit RTCB and the N-terminal domain of CGI-99. We show that the core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. The N-terminal domain of CGI-99 displays structural homology to calponin-homology domains, and CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. The crystal structure of GMP-bound RTCB reveals divalent metal coordination geometry in the active site, providing insights into its catalytic mechanism. Collectively, these findings shed light on the molecular architecture and mechanism of the human tRNA ligase complex and provide a structural framework for understanding its functions in cellular RNA metabolism.

Los videojuegos son una nueva forma de entretenimiento masivo que cada vez más personas encuadran dentro de una nueva forma de deporte. En esta revisión se trata de dilucidar cuál es el estado de debate acerca de la relación entre uso de videojuegos violentos, violencia y variables relacionadas. Para ello se revisaron las bases de datos MEDLINE complete, Psychology and Behavioral Science Collection, Psychoinfo y Sportdiscuss. El volumen total de referencias fue de 2.000 documentos publicados desde el año 2013 al 2019, de los que se seleccionaron 20 trabajos representativos sobre la temática. Los resultados de estas investigaciones señalaron que las consecuencias violentas o similares de los jugadores se deben a variables personales (ira rasgo y edad, principalmente en etapa de adolescencia y joven adultez) y contextuales (competición) que median entre el videojuego y la conducta problema. Se concluye que son estos moderadores los que explican la relación entre video juegos violentos, violencia y variables relacionadas, y no el contenido de los videojuegos.

Aging is associated with complex molecular and cellular processes that are poorly understood. Here we leveraged the Tabula Muris Senis single-cell RNA-seq data set to systematically characterize gene expression changes during aging across diverse cell types in the mouse. We identified aging-dependent genes in 76 tissue-cell types from 23 tissues and characterized both shared and tissue-cell-specific aging behaviors. We found that the aging-related genes shared by multiple tissue-cell types also change their expression congruently in the same direction during aging in most tissue-cell types, suggesting a coordinated global aging behavior at the organismal level. Scoring cells based on these shared aging genes allowed us to contrast the aging status of different tissues and cell types from a transcriptomic perspective. In addition, we identified genes that exhibit age-related expression changes specific to each functional category of tissue-cell types. Altogether, our analyses provide one of the most comprehensive and systematic characterizations of the molecular signatures of aging across diverse tissue-cell types in a mammalian system.

Fungi are a highly diverse group of organisms and play a significant role in decomposition and carbon cycling in boreal ecosystems. To determine how fungal communities are structured in peat bogs and how to obtain representative samples for monitoring fungal community changes, we separately sampled and sequenced (ITS2, Illumina MiSeq) peat, mixed litter and litter from individual dominant plant species in five permanent plots in raised bogs in the Jizerské Hory Mountains (Czech Republic). In total, we detected 68–103 OTUs per plot. The fungal assemblages were mostly influenced by substrate identity, whereas the effect of the site was minimal. Only a few identified OTUs behave like generalists. The most specific fungi were found in dead parts of Calluna vulgaris, Trichophorum cespitosum and Drosera rotundifolia. The high substrate heterogeneity means that sequencing soil core samples does not provide an exhaustive inventory of the fungal diversity in bogs. Poor correspondence was observed between the recorded OTUs and either visually inspected fruitbodies or literature reports on the fungal taxa associated with the analysed substrates.

Purpose. To describe a temporal approach, digitally assisted phacovitrectomy in a patient with severe kyphosis due to axial spondyloarthritis. Case Report. A 70-year-old male patient with proliferative diabetic retinopathy with vitreous hemorrhage and cataract and ankylosing spondylitis with severe kyphosis. A temporal approach, digitally assisted 25 G phacovitrectomy was performed with a Constellation platform and the NGENUITY visualization system. The Trendelenburg position was utilized. Conclusion. A temporal approach, digitally assisted phacovitrectomy may be used in select cases of severe kyphosis with positive outcomes.

Macular hole retinal detachment (MHRD) for the most part develops in highly myopic eyes. Several surgical methods have been introduced to treat MHRD. We describe our experience with the autologous retinal transplant in patient with MHRD. A 49-year-old female presented with a 2-week history of a sudden decrease in the central vision in the right eye (RE). A 3-port, 25-gauge pars plana vitrectomy was performed with the ILM dye staining and peeling. Endodiathermy was applied around a 1.5-disc diameter neurosensory donor site in the supertemporal retina. The graft was cut with standard 25-gauge curved scissors. Perfluoro-n-octane (PFO) was instilled. The free graft was gently handled until its packing into the macular hole. Two months following the initial PPV, the macular hole was closed, and vision improved from 0.05 to 0.25 logMAR.

Reduction of gaseous Hg(II) compounds drives atmospheric mercury wet and dry deposition to Earth surface ecosystems. Global Hg models assume this reduction takes place in clouds. Here the authors report a new gas-phase Hg photochemical mechanism that changes atmospheric mercury lifetime and its deposition to the surface.